Starting phenix.real_space_refine (version: dev) on Sat Dec 17 00:39:54 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ope_13017/12_2022/7ope_13017.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ope_13017/12_2022/7ope_13017.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ope_13017/12_2022/7ope_13017.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ope_13017/12_2022/7ope_13017.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ope_13017/12_2022/7ope_13017.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ope_13017/12_2022/7ope_13017.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "G TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 3": "NH1" <-> "NH2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "H ARG 69": "NH1" <-> "NH2" Residue "H ARG 78": "NH1" <-> "NH2" Residue "H ARG 80": "NH1" <-> "NH2" Residue "H GLU 81": "OE1" <-> "OE2" Residue "H ARG 92": "NH1" <-> "NH2" Residue "H GLU 94": "OE1" <-> "OE2" Residue "H ARG 110": "NH1" <-> "NH2" Residue "H ARG 112": "NH1" <-> "NH2" Residue "H ARG 115": "NH1" <-> "NH2" Residue "H GLU 164": "OE1" <-> "OE2" Residue "H GLU 165": "OE1" <-> "OE2" Residue "1 GLU 62": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 93862 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 60436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2814, 60436 Classifications: {'RNA': 2814} Modifications used: {'5*END': 1, 'rna2p_pur': 282, 'rna2p_pyr': 144, 'rna3p_pur': 1354, 'rna3p_pyr': 1034} Link IDs: {'rna2p': 426, 'rna3p': 2387} Chain breaks: 6 Chain: "B" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 2392 Classifications: {'RNA': 112} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 52, 'rna3p_pyr': 46} Link IDs: {'rna2p': 14, 'rna3p': 97} Chain: "E" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2083 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 17, 'TRANS': 254} Chain: "F" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1569 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 10, 'TRANS': 195} Chain: "G" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1561 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain: "H" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1387 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 7, 'TRANS': 168} Chain: "I" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1342 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 9, 'TRANS': 165} Chain: "K" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 974 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 10, 'TRANS': 121} Chain: "L" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 886 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain breaks: 2 Chain: "N" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1124 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 133} Chain: "O" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 921 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "P" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1082 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 140} Chain: "Q" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1076 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain: "R" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 954 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "S" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 913 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain: "T" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 945 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "U" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 940 Classifications: {'peptide': 117} Link IDs: {'TRANS': 116} Chain: "V" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 781 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "W" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "X" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 725 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "Y" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 762 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "2" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 1496 Classifications: {'RNA': 70} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 29, 'rna3p_pyr': 29} Link IDs: {'rna2p': 11, 'rna3p': 58} Chain breaks: 2 Chain: "a" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 624 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "b" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "c" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 530 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "d" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 456 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "f" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 418 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 3, 'TRANS': 49} Chain: "g" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 401 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "h" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 368 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "i" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 512 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "j" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 297 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "1" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 659 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "0" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 3962 Classifications: {'peptide': 532} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PTRANS': 26, 'TRANS': 505} Chain breaks: 6 Unresolved non-hydrogen bonds: 341 Unresolved non-hydrogen angles: 442 Unresolved non-hydrogen dihedrals: 278 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 9, 'TYR:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 5, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 187 Time building chain proxies: 39.40, per 1000 atoms: 0.42 Number of scatterers: 93862 At special positions: 0 Unit cell: (223.04, 227.96, 201.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 102 16.00 P 2994 15.00 O 26140 8.00 N 17431 7.00 C 47195 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS f 30 " - pdb=" SG CYS f 43 " distance=2.03 Simple disulfide: pdb=" SG CYS f 33 " - pdb=" SG CYS f 46 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 40.32 Conformation dependent library (CDL) restraints added in 3.6 seconds 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7006 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 53 sheets defined 32.2% alpha, 19.5% beta 1022 base pairs and 1624 stacking pairs defined. Time for finding SS restraints: 30.47 Creating SS restraints... Processing helix chain 'E' and resid 207 through 214 removed outlier: 4.126A pdb=" N SER E 211 " --> pdb=" O LYS E 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 71 Processing helix chain 'F' and resid 98 through 102 removed outlier: 3.676A pdb=" N ILE F 101 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 127 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 102 through 121 Processing helix chain 'G' and resid 135 through 146 removed outlier: 3.988A pdb=" N MET G 139 " --> pdb=" O LYS G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 166 Processing helix chain 'G' and resid 179 through 181 No H-bonds generated for 'chain 'G' and resid 179 through 181' Processing helix chain 'G' and resid 183 through 189 Processing helix chain 'G' and resid 195 through 206 Processing helix chain 'H' and resid 4 through 11 Processing helix chain 'H' and resid 11 through 21 Processing helix chain 'H' and resid 24 through 28 Processing helix chain 'H' and resid 41 through 44 removed outlier: 3.605A pdb=" N VAL H 44 " --> pdb=" O GLY H 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 41 through 44' Processing helix chain 'H' and resid 46 through 62 removed outlier: 3.795A pdb=" N ILE H 50 " --> pdb=" O ASN H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 78 Processing helix chain 'H' and resid 92 through 106 removed outlier: 3.516A pdb=" N MET H 96 " --> pdb=" O ARG H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 111 Processing helix chain 'H' and resid 134 through 138 removed outlier: 3.774A pdb=" N ILE H 137 " --> pdb=" O GLU H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 173 removed outlier: 3.709A pdb=" N VAL H 173 " --> pdb=" O LEU H 169 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 82 removed outlier: 3.747A pdb=" N ALA I 64 " --> pdb=" O LYS I 60 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG I 70 " --> pdb=" O HIS I 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 151 Processing helix chain 'K' and resid 20 through 30 removed outlier: 4.214A pdb=" N VAL K 24 " --> pdb=" O PRO K 20 " (cutoff:3.500A) Proline residue: K 26 - end of helix removed outlier: 3.878A pdb=" N GLN K 30 " --> pdb=" O PRO K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 46 Processing helix chain 'K' and resid 74 through 84 Processing helix chain 'K' and resid 102 through 113 Processing helix chain 'K' and resid 120 through 136 Processing helix chain 'L' and resid 6 through 22 Processing helix chain 'L' and resid 34 through 49 Processing helix chain 'L' and resid 56 through 65 Processing helix chain 'L' and resid 73 through 77 removed outlier: 3.780A pdb=" N THR L 77 " --> pdb=" O ASP L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 93 through 104 Processing helix chain 'L' and resid 119 through 128 Processing helix chain 'N' and resid 25 through 39 removed outlier: 4.124A pdb=" N GLU N 32 " --> pdb=" O ARG N 28 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA N 35 " --> pdb=" O SER N 31 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 63 Processing helix chain 'N' and resid 68 through 73 Processing helix chain 'N' and resid 90 through 97 Processing helix chain 'N' and resid 97 through 110 removed outlier: 4.114A pdb=" N MET N 101 " --> pdb=" O TYR N 97 " (cutoff:3.500A) Processing helix chain 'N' and resid 113 through 121 Processing helix chain 'O' and resid 103 through 107 removed outlier: 3.900A pdb=" N LEU O 106 " --> pdb=" O ALA O 103 " (cutoff:3.500A) Processing helix chain 'O' and resid 111 through 118 Processing helix chain 'P' and resid 56 through 61 Processing helix chain 'P' and resid 80 through 85 removed outlier: 3.654A pdb=" N GLY P 84 " --> pdb=" O LYS P 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 92 through 100 Processing helix chain 'P' and resid 129 through 140 Processing helix chain 'Q' and resid 44 through 59 Processing helix chain 'Q' and resid 110 through 125 Processing helix chain 'R' and resid 9 through 28 Processing helix chain 'R' and resid 34 through 54 removed outlier: 4.240A pdb=" N SER R 42 " --> pdb=" O LYS R 38 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL R 43 " --> pdb=" O GLU R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 66 Processing helix chain 'R' and resid 79 through 91 Processing helix chain 'S' and resid 6 through 20 Processing helix chain 'S' and resid 70 through 88 Processing helix chain 'S' and resid 104 through 117 Processing helix chain 'T' and resid 2 through 10 Processing helix chain 'T' and resid 53 through 56 Processing helix chain 'U' and resid 7 through 21 removed outlier: 4.067A pdb=" N ARG U 11 " --> pdb=" O GLY U 7 " (cutoff:3.500A) Processing helix chain 'U' and resid 26 through 31 Processing helix chain 'U' and resid 31 through 73 removed outlier: 3.570A pdb=" N GLN U 38 " --> pdb=" O VAL U 34 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS U 41 " --> pdb=" O GLN U 37 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG U 51 " --> pdb=" O PHE U 47 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LYS U 54 " --> pdb=" O ARG U 50 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG U 55 " --> pdb=" O ARG U 51 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG U 58 " --> pdb=" O LYS U 54 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS U 59 " --> pdb=" O ARG U 55 " (cutoff:3.500A) Processing helix chain 'U' and resid 75 through 87 Processing helix chain 'U' and resid 91 through 101 Processing helix chain 'U' and resid 102 through 117 removed outlier: 3.542A pdb=" N PHE U 106 " --> pdb=" O ASP U 102 " (cutoff:3.500A) Processing helix chain 'W' and resid 13 through 25 removed outlier: 3.767A pdb=" N ALA W 17 " --> pdb=" O ALA W 13 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE W 24 " --> pdb=" O VAL W 20 " (cutoff:3.500A) Processing helix chain 'W' and resid 28 through 39 Processing helix chain 'W' and resid 43 through 62 Processing helix chain 'W' and resid 65 through 67 No H-bonds generated for 'chain 'W' and resid 65 through 67' Processing helix chain 'X' and resid 3 through 7 Processing helix chain 'X' and resid 14 through 23 removed outlier: 3.565A pdb=" N GLU X 23 " --> pdb=" O ASP X 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 35 through 48 Processing helix chain 'b' and resid 20 through 22 No H-bonds generated for 'chain 'b' and resid 20 through 22' Processing helix chain 'b' and resid 51 through 55 Processing helix chain 'c' and resid 2 through 8 Processing helix chain 'c' and resid 12 through 35 Processing helix chain 'c' and resid 40 through 65 removed outlier: 4.159A pdb=" N ARG c 44 " --> pdb=" O THR c 40 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE c 57 " --> pdb=" O MET c 53 " (cutoff:3.500A) Processing helix chain 'd' and resid 16 through 27 Processing helix chain 'd' and resid 40 through 51 Processing helix chain 'f' and resid 9 through 17 Processing helix chain 'h' and resid 8 through 16 Processing helix chain 'h' and resid 17 through 24 removed outlier: 3.626A pdb=" N SER h 24 " --> pdb=" O SER h 20 " (cutoff:3.500A) Processing helix chain 'h' and resid 24 through 37 Processing helix chain 'i' and resid 7 through 14 Processing helix chain 'i' and resid 37 through 45 Processing helix chain 'i' and resid 51 through 59 Processing helix chain 'i' and resid 60 through 63 removed outlier: 3.868A pdb=" N ALA i 63 " --> pdb=" O GLN i 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 60 through 63' Processing helix chain 'j' and resid 29 through 32 Processing helix chain '1' and resid 2 through 10 Processing helix chain '1' and resid 15 through 26 Processing helix chain '1' and resid 70 through 74 removed outlier: 3.532A pdb=" N ALA 1 73 " --> pdb=" O GLU 1 70 " (cutoff:3.500A) Processing helix chain '0' and resid 4 through 17 Processing helix chain '0' and resid 73 through 84 removed outlier: 3.556A pdb=" N GLU 0 84 " --> pdb=" O ARG 0 80 " (cutoff:3.500A) Processing helix chain '0' and resid 147 through 151 removed outlier: 3.597A pdb=" N MET 0 150 " --> pdb=" O SER 0 147 " (cutoff:3.500A) Processing helix chain '0' and resid 180 through 185 Processing helix chain '0' and resid 186 through 190 removed outlier: 3.700A pdb=" N GLY 0 190 " --> pdb=" O PHE 0 187 " (cutoff:3.500A) Processing helix chain '0' and resid 191 through 196 removed outlier: 4.000A pdb=" N GLN 0 195 " --> pdb=" O ARG 0 191 " (cutoff:3.500A) Processing helix chain '0' and resid 204 through 213 Processing helix chain '0' and resid 223 through 236 removed outlier: 3.977A pdb=" N LEU 0 227 " --> pdb=" O LEU 0 223 " (cutoff:3.500A) Processing helix chain '0' and resid 269 through 277 Processing helix chain '0' and resid 283 through 317 removed outlier: 3.605A pdb=" N PHE 0 297 " --> pdb=" O ASP 0 293 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU 0 317 " --> pdb=" O GLU 0 313 " (cutoff:3.500A) Processing helix chain '0' and resid 321 through 335 removed outlier: 3.691A pdb=" N PHE 0 325 " --> pdb=" O ASN 0 321 " (cutoff:3.500A) Processing helix chain '0' and resid 368 through 413 Processing helix chain '0' and resid 415 through 429 removed outlier: 3.984A pdb=" N GLU 0 421 " --> pdb=" O ARG 0 417 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU 0 424 " --> pdb=" O SER 0 420 " (cutoff:3.500A) Processing helix chain '0' and resid 456 through 458 No H-bonds generated for 'chain '0' and resid 456 through 458' Processing helix chain '0' and resid 466 through 477 Processing helix chain '0' and resid 503 through 517 removed outlier: 3.593A pdb=" N ALA 0 511 " --> pdb=" O ILE 0 507 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR 0 512 " --> pdb=" O MET 0 508 " (cutoff:3.500A) Processing helix chain '0' and resid 534 through 536 No H-bonds generated for 'chain '0' and resid 534 through 536' Processing helix chain '0' and resid 561 through 565 Processing sheet with id=AA1, first strand: chain 'E' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'E' and resid 34 through 35 Processing sheet with id=AA3, first strand: chain 'E' and resid 101 through 105 removed outlier: 6.612A pdb=" N ILE E 91 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N VAL E 81 " --> pdb=" O ILE E 91 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU E 93 " --> pdb=" O ALA E 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 129 through 131 removed outlier: 6.702A pdb=" N LEU E 173 " --> pdb=" O LEU E 165 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N LYS E 167 " --> pdb=" O TYR E 171 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N TYR E 171 " --> pdb=" O LYS E 167 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 4 through 14 removed outlier: 5.391A pdb=" N LYS F 9 " --> pdb=" O GLU F 29 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N GLU F 29 " --> pdb=" O LYS F 9 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY F 11 " --> pdb=" O VAL F 27 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU F 185 " --> pdb=" O VAL F 179 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL F 179 " --> pdb=" O LEU F 185 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU F 187 " --> pdb=" O VAL F 177 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLU F 175 " --> pdb=" O LYS F 189 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N VAL F 108 " --> pdb=" O ASN F 173 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N VAL F 113 " --> pdb=" O LEU F 199 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU F 199 " --> pdb=" O VAL F 113 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 79 through 84 removed outlier: 3.678A pdb=" N PHE F 79 " --> pdb=" O PHE F 53 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA F 48 " --> pdb=" O LYS F 39 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLN F 37 " --> pdb=" O GLN F 50 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLY F 52 " --> pdb=" O VAL F 35 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N VAL F 35 " --> pdb=" O GLY F 52 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 116 through 120 Processing sheet with id=AA8, first strand: chain 'G' and resid 13 through 18 removed outlier: 5.661A pdb=" N GLY G 15 " --> pdb=" O LEU G 6 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU G 6 " --> pdb=" O GLY G 15 " (cutoff:3.500A) removed outlier: 11.508A pdb=" N ILE G 123 " --> pdb=" O LYS G 3 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA G 5 " --> pdb=" O ILE G 123 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL G 125 " --> pdb=" O ALA G 5 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU G 153 " --> pdb=" O LEU G 193 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA G 152 " --> pdb=" O THR G 174 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N VAL G 176 " --> pdb=" O ALA G 152 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ILE G 154 " --> pdb=" O VAL G 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 66 through 69 Processing sheet with id=AB1, first strand: chain 'I' and resid 9 through 10 Processing sheet with id=AB2, first strand: chain 'I' and resid 16 through 19 Processing sheet with id=AB3, first strand: chain 'I' and resid 123 through 125 Processing sheet with id=AB4, first strand: chain 'I' and resid 96 through 98 Processing sheet with id=AB5, first strand: chain 'K' and resid 10 through 14 removed outlier: 3.613A pdb=" N SER K 65 " --> pdb=" O TYR K 61 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 98 through 101 Processing sheet with id=AB7, first strand: chain 'L' and resid 51 through 54 Processing sheet with id=AB8, first strand: chain 'N' and resid 123 through 125 removed outlier: 6.414A pdb=" N TRP N 16 " --> pdb=" O GLU N 139 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 74 through 78 Processing sheet with id=AC1, first strand: chain 'O' and resid 7 through 10 removed outlier: 6.286A pdb=" N ARG O 17 " --> pdb=" O VAL O 10 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA O 16 " --> pdb=" O ALA O 46 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ALA O 46 " --> pdb=" O ALA O 16 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLU O 18 " --> pdb=" O LYS O 44 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL O 40 " --> pdb=" O ILE O 22 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N VAL O 24 " --> pdb=" O VAL O 38 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N VAL O 38 " --> pdb=" O VAL O 24 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA O 83 " --> pdb=" O VAL O 63 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N CYS O 84 " --> pdb=" O ARG O 7 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LYS O 9 " --> pdb=" O CYS O 84 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ILE O 86 " --> pdb=" O LYS O 9 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'O' and resid 76 through 79 removed outlier: 6.720A pdb=" N THR T 58 " --> pdb=" O ARG T 50 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ARG T 50 " --> pdb=" O THR T 58 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR T 60 " --> pdb=" O ILE T 48 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ILE T 64 " --> pdb=" O GLU T 44 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N GLU T 44 " --> pdb=" O ILE T 64 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ASP T 24 " --> pdb=" O VAL T 47 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR T 25 " --> pdb=" O VAL T 87 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS T 83 " --> pdb=" O HIS T 29 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LYS T 31 " --> pdb=" O ILE T 81 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE T 81 " --> pdb=" O LYS T 31 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'P' and resid 75 through 77 removed outlier: 6.053A pdb=" N ALA P 75 " --> pdb=" O LYS P 110 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N VAL P 109 " --> pdb=" O LYS P 127 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'P' and resid 90 through 91 removed outlier: 6.303A pdb=" N VAL P 123 " --> pdb=" O GLU P 144 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Q' and resid 102 through 104 removed outlier: 6.665A pdb=" N VAL Q 102 " --> pdb=" O ALA Q 36 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA Q 36 " --> pdb=" O VAL Q 102 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE Q 104 " --> pdb=" O ILE Q 34 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Q' and resid 40 through 43 removed outlier: 5.391A pdb=" N ALA Q 76 " --> pdb=" O PRO Q 90 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY Q 92 " --> pdb=" O TYR Q 74 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR Q 74 " --> pdb=" O GLY Q 92 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'R' and resid 29 through 33 removed outlier: 4.273A pdb=" N MET R 114 " --> pdb=" O LEU R 104 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'R' and resid 70 through 72 removed outlier: 3.702A pdb=" N ASN R 72 " --> pdb=" O GLN R 77 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'S' and resid 51 through 57 removed outlier: 6.747A pdb=" N ILE S 44 " --> pdb=" O LEU S 53 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N SER S 55 " --> pdb=" O ALA S 42 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA S 42 " --> pdb=" O SER S 55 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL S 33 " --> pdb=" O ASP S 96 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'V' and resid 11 through 14 Processing sheet with id=AD2, first strand: chain 'V' and resid 19 through 22 removed outlier: 3.573A pdb=" N LYS V 64 " --> pdb=" O LYS V 94 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N THR V 96 " --> pdb=" O VAL V 62 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N VAL V 62 " --> pdb=" O THR V 96 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N GLU V 98 " --> pdb=" O ALA V 60 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ALA V 60 " --> pdb=" O GLU V 98 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE V 100 " --> pdb=" O VAL V 58 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL V 58 " --> pdb=" O ILE V 100 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'V' and resid 71 through 75 Processing sheet with id=AD4, first strand: chain 'W' and resid 3 through 10 removed outlier: 6.337A pdb=" N SER W 101 " --> pdb=" O THR W 9 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N SER W 108 " --> pdb=" O ILE W 71 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ILE W 71 " --> pdb=" O SER W 108 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'W' and resid 82 through 87 Processing sheet with id=AD6, first strand: chain 'X' and resid 8 through 10 removed outlier: 4.013A pdb=" N ARG X 77 " --> pdb=" O VAL X 30 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Y' and resid 20 through 21 Processing sheet with id=AD8, first strand: chain 'Y' and resid 23 through 27 removed outlier: 4.220A pdb=" N ALA Y 25 " --> pdb=" O LEU Y 34 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Y' and resid 40 through 44 Processing sheet with id=AE1, first strand: chain 'Y' and resid 81 through 85 removed outlier: 3.949A pdb=" N GLN Y 99 " --> pdb=" O ALA Y 94 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'a' and resid 30 through 31 removed outlier: 6.851A pdb=" N LEU a 67 " --> pdb=" O LEU a 45 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'a' and resid 38 through 39 Processing sheet with id=AE4, first strand: chain 'b' and resid 13 through 18 Processing sheet with id=AE5, first strand: chain 'b' and resid 33 through 36 Processing sheet with id=AE6, first strand: chain 'd' and resid 35 through 38 Processing sheet with id=AE7, first strand: chain 'f' and resid 27 through 29 Processing sheet with id=AE8, first strand: chain 'f' and resid 48 through 49 Processing sheet with id=AE9, first strand: chain 'g' and resid 18 through 22 Processing sheet with id=AF1, first strand: chain 'i' and resid 15 through 16 Processing sheet with id=AF2, first strand: chain 'j' and resid 2 through 3 removed outlier: 6.122A pdb=" N LYS j 2 " --> pdb=" O LYS j 35 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN j 34 " --> pdb=" O VAL j 25 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain '1' and resid 33 through 34 removed outlier: 6.843A pdb=" N LEU 1 55 " --> pdb=" O GLU 1 81 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLU 1 81 " --> pdb=" O LEU 1 55 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR 1 57 " --> pdb=" O LEU 1 79 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain '0' and resid 23 through 31 removed outlier: 6.586A pdb=" N HIS 0 38 " --> pdb=" O THR 0 25 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE 0 27 " --> pdb=" O ILE 0 36 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE 0 36 " --> pdb=" O ILE 0 27 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLN 0 29 " --> pdb=" O ASP 0 34 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ASP 0 34 " --> pdb=" O GLN 0 29 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain '0' and resid 87 through 92 removed outlier: 5.394A pdb=" N ILE 0 88 " --> pdb=" O LYS 0 105 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LYS 0 105 " --> pdb=" O ILE 0 88 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ILE 0 129 " --> pdb=" O GLY 0 142 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLY 0 142 " --> pdb=" O ILE 0 129 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU 0 131 " --> pdb=" O ILE 0 140 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain '0' and resid 250 through 253 removed outlier: 3.651A pdb=" N TYR 0 253 " --> pdb=" O ASN 0 242 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN 0 242 " --> pdb=" O TYR 0 253 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain '0' and resid 345 through 349 Processing sheet with id=AF8, first strand: chain '0' and resid 451 through 454 removed outlier: 3.530A pdb=" N TYR 0 453 " --> pdb=" O ILE 0 461 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE 0 461 " --> pdb=" O TYR 0 453 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY 0 464 " --> pdb=" O HIS 0 494 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N HIS 0 494 " --> pdb=" O GLY 0 464 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ILE 0 497 " --> pdb=" O ILE 0 483 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE 0 483 " --> pdb=" O ILE 0 497 " (cutoff:3.500A) 1219 hydrogen bonds defined for protein. 3399 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2605 hydrogen bonds 4244 hydrogen bond angles 0 basepair planarities 1022 basepair parallelities 1624 stacking parallelities Total time for adding SS restraints: 158.21 Time building geometry restraints manager: 43.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 7798 1.29 - 1.43: 45927 1.43 - 1.56: 42046 1.56 - 1.70: 6004 1.70 - 1.83: 189 Bond restraints: 101964 Sorted by residual: bond pdb=" C VAL 1 58 " pdb=" N GLN 1 59 " ideal model delta sigma weight residual 1.331 1.458 -0.128 1.34e-02 5.57e+03 9.06e+01 bond pdb=" C1' U A1940 " pdb=" N1 U A1940 " ideal model delta sigma weight residual 1.480 1.587 -0.107 1.50e-02 4.44e+03 5.08e+01 bond pdb=" C LEU H 170 " pdb=" O LEU H 170 " ideal model delta sigma weight residual 1.237 1.158 0.079 1.19e-02 7.06e+03 4.40e+01 bond pdb=" P G A1220 " pdb=" OP2 G A1220 " ideal model delta sigma weight residual 1.485 1.610 -0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" P G A1220 " pdb=" OP1 G A1220 " ideal model delta sigma weight residual 1.485 1.610 -0.125 2.00e-02 2.50e+03 3.90e+01 ... (remaining 101959 not shown) Histogram of bond angle deviations from ideal: 56.69 - 74.74: 1 74.74 - 92.80: 5 92.80 - 110.85: 57817 110.85 - 128.91: 90616 128.91 - 146.97: 4048 Bond angle restraints: 152487 Sorted by residual: angle pdb=" C ILE 0 490 " pdb=" N PRO 0 491 " pdb=" CD PRO 0 491 " ideal model delta sigma weight residual 125.00 56.69 68.31 4.10e+00 5.95e-02 2.78e+02 angle pdb=" O3' G A1939 " pdb=" P U A1940 " pdb=" O5' U A1940 " ideal model delta sigma weight residual 104.00 84.73 19.27 1.50e+00 4.44e-01 1.65e+02 angle pdb=" C3' A A1947 " pdb=" C2' A A1947 " pdb=" O2' A A1947 " ideal model delta sigma weight residual 114.60 98.69 15.91 1.50e+00 4.44e-01 1.13e+02 angle pdb=" O3' A A1947 " pdb=" C3' A A1947 " pdb=" C2' A A1947 " ideal model delta sigma weight residual 109.50 124.95 -15.45 1.50e+00 4.44e-01 1.06e+02 angle pdb=" O3' C 2 48 " pdb=" P A 2 49 " pdb=" OP1 A 2 49 " ideal model delta sigma weight residual 108.00 77.72 30.28 3.00e+00 1.11e-01 1.02e+02 ... (remaining 152482 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 52565 35.88 - 71.77: 1815 71.77 - 107.65: 148 107.65 - 143.54: 35 143.54 - 179.42: 45 Dihedral angle restraints: 54608 sinusoidal: 43737 harmonic: 10871 Sorted by residual: dihedral pdb=" CA ASN V 50 " pdb=" C ASN V 50 " pdb=" N PRO V 51 " pdb=" CA PRO V 51 " ideal model delta harmonic sigma weight residual 180.00 129.53 50.47 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" O4' U A2105 " pdb=" C1' U A2105 " pdb=" N1 U A2105 " pdb=" C2 U A2105 " ideal model delta sinusoidal sigma weight residual 200.00 26.52 173.48 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' U A 794 " pdb=" C1' U A 794 " pdb=" N1 U A 794 " pdb=" C2 U A 794 " ideal model delta sinusoidal sigma weight residual 200.00 33.05 166.95 1 1.50e+01 4.44e-03 8.42e+01 ... (remaining 54605 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.179: 19300 0.179 - 0.357: 189 0.357 - 0.536: 7 0.536 - 0.715: 1 0.715 - 0.893: 2 Chirality restraints: 19499 Sorted by residual: chirality pdb=" P A 2 49 " pdb=" OP1 A 2 49 " pdb=" OP2 A 2 49 " pdb=" O5' A 2 49 " both_signs ideal model delta sigma weight residual True 2.41 1.52 0.89 2.00e-01 2.50e+01 1.99e+01 chirality pdb=" P G A1220 " pdb=" OP1 G A1220 " pdb=" OP2 G A1220 " pdb=" O5' G A1220 " both_signs ideal model delta sigma weight residual True 2.41 -3.21 -0.80 2.00e-01 2.50e+01 1.60e+01 chirality pdb=" P G 2 19 " pdb=" OP1 G 2 19 " pdb=" OP2 G 2 19 " pdb=" O5' G 2 19 " both_signs ideal model delta sigma weight residual True 2.41 -2.97 -0.56 2.00e-01 2.50e+01 7.95e+00 ... (remaining 19496 not shown) Planarity restraints: 8177 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U A2334 " 0.450 2.00e-02 2.50e+03 2.07e-01 9.68e+02 pdb=" N1 U A2334 " -0.146 2.00e-02 2.50e+03 pdb=" C2 U A2334 " -0.096 2.00e-02 2.50e+03 pdb=" O2 U A2334 " -0.164 2.00e-02 2.50e+03 pdb=" N3 U A2334 " 0.062 2.00e-02 2.50e+03 pdb=" C4 U A2334 " 0.060 2.00e-02 2.50e+03 pdb=" O4 U A2334 " 0.205 2.00e-02 2.50e+03 pdb=" C5 U A2334 " -0.117 2.00e-02 2.50e+03 pdb=" C6 U A2334 " -0.254 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A2338 " 0.335 2.00e-02 2.50e+03 1.37e-01 5.14e+02 pdb=" N9 A A2338 " -0.085 2.00e-02 2.50e+03 pdb=" C8 A A2338 " -0.102 2.00e-02 2.50e+03 pdb=" N7 A A2338 " -0.071 2.00e-02 2.50e+03 pdb=" C5 A A2338 " -0.047 2.00e-02 2.50e+03 pdb=" C6 A A2338 " 0.056 2.00e-02 2.50e+03 pdb=" N6 A A2338 " 0.168 2.00e-02 2.50e+03 pdb=" N1 A A2338 " 0.052 2.00e-02 2.50e+03 pdb=" C2 A A2338 " -0.057 2.00e-02 2.50e+03 pdb=" N3 A A2338 " -0.133 2.00e-02 2.50e+03 pdb=" C4 A A2338 " -0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 2 23 " -0.292 2.00e-02 2.50e+03 1.24e-01 4.24e+02 pdb=" N9 A 2 23 " 0.043 2.00e-02 2.50e+03 pdb=" C8 A 2 23 " 0.075 2.00e-02 2.50e+03 pdb=" N7 A 2 23 " 0.067 2.00e-02 2.50e+03 pdb=" C5 A 2 23 " 0.073 2.00e-02 2.50e+03 pdb=" C6 A 2 23 " -0.029 2.00e-02 2.50e+03 pdb=" N6 A 2 23 " -0.176 2.00e-02 2.50e+03 pdb=" N1 A 2 23 " -0.049 2.00e-02 2.50e+03 pdb=" C2 A 2 23 " 0.035 2.00e-02 2.50e+03 pdb=" N3 A 2 23 " 0.127 2.00e-02 2.50e+03 pdb=" C4 A 2 23 " 0.125 2.00e-02 2.50e+03 ... (remaining 8174 not shown) Histogram of nonbonded interaction distances: 1.03 - 1.80: 11 1.80 - 2.58: 1936 2.58 - 3.35: 114681 3.35 - 4.13: 314035 4.13 - 4.90: 446632 Nonbonded interactions: 877295 Sorted by model distance: nonbonded pdb=" C2 G 2 30 " pdb=" CZ ARG 0 125 " model vdw 1.028 3.490 nonbonded pdb=" N3 G 2 30 " pdb=" NE ARG 0 125 " model vdw 1.321 2.600 nonbonded pdb=" C2 G 2 30 " pdb=" NE ARG 0 125 " model vdw 1.373 3.340 nonbonded pdb=" N1 G 2 30 " pdb=" NH2 ARG 0 125 " model vdw 1.413 3.200 nonbonded pdb=" N1 G 2 30 " pdb=" CZ ARG 0 125 " model vdw 1.584 3.350 ... (remaining 877290 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2994 5.49 5 S 102 5.16 5 C 47195 2.51 5 N 17431 2.21 5 O 26140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 20.460 Check model and map are aligned: 1.040 Convert atoms to be neutral: 0.610 Process input model: 333.400 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 364.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.194 101964 Z= 0.697 Angle : 1.042 68.312 152487 Z= 0.552 Chirality : 0.058 0.893 19499 Planarity : 0.011 0.277 8177 Dihedral : 15.484 179.421 47596 Min Nonbonded Distance : 1.028 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.20 % Favored : 91.61 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.12), residues: 3742 helix: -1.63 (0.12), residues: 1143 sheet: -2.79 (0.16), residues: 700 loop : -2.74 (0.13), residues: 1899 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1453 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1446 time to evaluate : 5.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 1449 average time/residue: 0.9267 time to fit residues: 2214.1723 Evaluate side-chains 868 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 866 time to evaluate : 4.140 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 1.1479 time to fit residues: 7.9076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 564 optimal weight: 8.9990 chunk 506 optimal weight: 5.9990 chunk 280 optimal weight: 10.0000 chunk 172 optimal weight: 10.0000 chunk 341 optimal weight: 8.9990 chunk 270 optimal weight: 10.0000 chunk 523 optimal weight: 6.9990 chunk 202 optimal weight: 5.9990 chunk 318 optimal weight: 6.9990 chunk 389 optimal weight: 5.9990 chunk 606 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 86 ASN E 163 GLN E 194 GLN E 200 HIS ** E 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 GLN ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 GLN N 124 ASN O 45 GLN O 82 ASN ** O 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 110 ASN P 54 GLN P 70 ASN P 114 ASN R 12 GLN R 27 ASN ** R 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 81 GLN ** S 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 2 GLN ** U 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 2 GLN Y 99 GLN b 20 HIS b 34 GLN d 32 ASN d 37 HIS ** g 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 25 ASN ** j 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 126 HIS 0 145 HIS 0 151 ASN 0 307 ASN 0 326 GLN 0 335 ASN 0 385 ASN 0 393 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.117 101964 Z= 0.244 Angle : 0.741 33.287 152487 Z= 0.373 Chirality : 0.039 0.682 19499 Planarity : 0.006 0.153 8177 Dihedral : 16.142 179.843 40091 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 19.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.33 % Favored : 93.53 % Rotamer Outliers : 4.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.13), residues: 3742 helix: -0.32 (0.14), residues: 1149 sheet: -1.72 (0.17), residues: 699 loop : -2.11 (0.13), residues: 1894 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1165 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 1022 time to evaluate : 4.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 143 outliers final: 76 residues processed: 1082 average time/residue: 0.9014 time to fit residues: 1636.4531 Evaluate side-chains 904 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 828 time to evaluate : 4.206 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 0 residues processed: 76 average time/residue: 0.6853 time to fit residues: 102.7997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 337 optimal weight: 5.9990 chunk 188 optimal weight: 20.0000 chunk 504 optimal weight: 20.0000 chunk 413 optimal weight: 50.0000 chunk 167 optimal weight: 20.0000 chunk 607 optimal weight: 8.9990 chunk 656 optimal weight: 50.0000 chunk 541 optimal weight: 30.0000 chunk 602 optimal weight: 20.0000 chunk 207 optimal weight: 20.0000 chunk 487 optimal weight: 40.0000 overall best weight: 14.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 GLN E 194 GLN ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 135 HIS ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 GLN ** N 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 35 HIS ** P 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 27 ASN ** R 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 GLN ** U 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 20 HIS c 27 ASN ** g 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 305 ASN ** 0 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.093 101964 Z= 0.470 Angle : 0.909 35.129 152487 Z= 0.464 Chirality : 0.048 1.245 19499 Planarity : 0.007 0.094 8177 Dihedral : 17.050 179.047 40091 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 41.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.26 % Favored : 91.61 % Rotamer Outliers : 5.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.13), residues: 3742 helix: -0.43 (0.14), residues: 1142 sheet: -1.67 (0.17), residues: 752 loop : -2.13 (0.13), residues: 1848 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1011 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 831 time to evaluate : 4.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 180 outliers final: 125 residues processed: 928 average time/residue: 0.8986 time to fit residues: 1418.0564 Evaluate side-chains 837 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 712 time to evaluate : 4.190 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 125 outliers final: 1 residues processed: 125 average time/residue: 0.7134 time to fit residues: 170.6115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 600 optimal weight: 8.9990 chunk 456 optimal weight: 7.9990 chunk 315 optimal weight: 7.9990 chunk 67 optimal weight: 20.0000 chunk 290 optimal weight: 10.0000 chunk 408 optimal weight: 50.0000 chunk 609 optimal weight: 6.9990 chunk 645 optimal weight: 30.0000 chunk 318 optimal weight: 10.0000 chunk 578 optimal weight: 5.9990 chunk 174 optimal weight: 20.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 14 GLN F 135 HIS H 21 ASN ** H 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 35 HIS ** P 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 72 ASN ** S 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 2 GLN ** Y 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 16 GLN g 16 ASN g 26 ASN ** j 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 101964 Z= 0.257 Angle : 0.709 24.589 152487 Z= 0.365 Chirality : 0.042 2.207 19499 Planarity : 0.005 0.070 8177 Dihedral : 16.797 179.673 40091 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 26.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.06 % Favored : 92.86 % Rotamer Outliers : 3.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.13), residues: 3742 helix: -0.15 (0.15), residues: 1139 sheet: -1.25 (0.18), residues: 725 loop : -1.88 (0.14), residues: 1878 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 957 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 840 time to evaluate : 4.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 117 outliers final: 63 residues processed: 901 average time/residue: 0.9088 time to fit residues: 1396.1412 Evaluate side-chains 804 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 741 time to evaluate : 4.198 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 0 residues processed: 63 average time/residue: 0.7061 time to fit residues: 88.2643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 537 optimal weight: 20.0000 chunk 366 optimal weight: 30.0000 chunk 9 optimal weight: 20.0000 chunk 480 optimal weight: 0.9980 chunk 266 optimal weight: 20.0000 chunk 550 optimal weight: 6.9990 chunk 446 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 329 optimal weight: 7.9990 chunk 579 optimal weight: 6.9990 chunk 162 optimal weight: 30.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 GLN ** H 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 82 ASN P 35 HIS ** P 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 12 GLN R 72 ASN R 76 ASN ** S 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 61 ASN ** 0 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 38 HIS ** 0 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 372 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.4889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 101964 Z= 0.294 Angle : 0.730 24.584 152487 Z= 0.375 Chirality : 0.043 2.099 19499 Planarity : 0.005 0.068 8177 Dihedral : 16.936 179.941 40091 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 30.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.72 % Favored : 92.20 % Rotamer Outliers : 3.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.13), residues: 3742 helix: -0.12 (0.15), residues: 1134 sheet: -1.09 (0.19), residues: 719 loop : -1.85 (0.14), residues: 1889 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 791 time to evaluate : 4.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 108 outliers final: 62 residues processed: 855 average time/residue: 0.8906 time to fit residues: 1295.5454 Evaluate side-chains 792 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 730 time to evaluate : 5.699 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 0 residues processed: 62 average time/residue: 0.7222 time to fit residues: 86.9811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 217 optimal weight: 20.0000 chunk 581 optimal weight: 6.9990 chunk 127 optimal weight: 20.0000 chunk 379 optimal weight: 20.0000 chunk 159 optimal weight: 20.0000 chunk 646 optimal weight: 40.0000 chunk 536 optimal weight: 9.9990 chunk 299 optimal weight: 8.9990 chunk 53 optimal weight: 20.0000 chunk 213 optimal weight: 20.0000 chunk 339 optimal weight: 20.0000 overall best weight: 13.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 ASN ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 ASN ** L 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 35 HIS ** P 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 ASN ** S 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 29 HIS ** U 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 19 HIS ** g 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 36 GLN ** 0 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.5582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.092 101964 Z= 0.417 Angle : 0.843 24.685 152487 Z= 0.430 Chirality : 0.047 2.012 19499 Planarity : 0.006 0.084 8177 Dihedral : 17.498 179.924 40091 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 41.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.66 % Favored : 91.23 % Rotamer Outliers : 4.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.13), residues: 3742 helix: -0.45 (0.15), residues: 1136 sheet: -1.14 (0.19), residues: 677 loop : -2.01 (0.13), residues: 1929 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 884 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 750 time to evaluate : 4.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 134 outliers final: 91 residues processed: 819 average time/residue: 0.8610 time to fit residues: 1207.0672 Evaluate side-chains 793 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 702 time to evaluate : 4.220 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 91 outliers final: 1 residues processed: 91 average time/residue: 0.7134 time to fit residues: 124.0393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 623 optimal weight: 50.0000 chunk 72 optimal weight: 20.0000 chunk 368 optimal weight: 6.9990 chunk 471 optimal weight: 9.9990 chunk 365 optimal weight: 20.0000 chunk 544 optimal weight: 20.0000 chunk 360 optimal weight: 6.9990 chunk 643 optimal weight: 3.9990 chunk 402 optimal weight: 10.0000 chunk 392 optimal weight: 1.9990 chunk 297 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 GLN ** H 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 35 HIS ** P 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 86 GLN ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 2 GLN ** X 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 26 ASN ** h 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.5542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.083 101964 Z= 0.226 Angle : 0.703 25.484 152487 Z= 0.359 Chirality : 0.041 2.007 19499 Planarity : 0.005 0.069 8177 Dihedral : 17.142 179.721 40091 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 28.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.30 % Favored : 92.62 % Rotamer Outliers : 1.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.13), residues: 3742 helix: -0.26 (0.15), residues: 1146 sheet: -1.02 (0.19), residues: 722 loop : -1.82 (0.14), residues: 1874 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 781 time to evaluate : 4.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 32 residues processed: 807 average time/residue: 0.9203 time to fit residues: 1279.9373 Evaluate side-chains 729 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 697 time to evaluate : 4.237 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 32 outliers final: 1 residues processed: 32 average time/residue: 0.8357 time to fit residues: 53.1980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 398 optimal weight: 20.0000 chunk 257 optimal weight: 20.0000 chunk 384 optimal weight: 5.9990 chunk 193 optimal weight: 20.0000 chunk 126 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 chunk 409 optimal weight: 9.9990 chunk 438 optimal weight: 10.0000 chunk 318 optimal weight: 7.9990 chunk 60 optimal weight: 20.0000 chunk 506 optimal weight: 0.6980 overall best weight: 6.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 35 HIS ** P 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 ASN ** S 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 2 GLN ** X 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 25 ASN g 26 ASN ** 1 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.5686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 101964 Z= 0.252 Angle : 0.719 26.500 152487 Z= 0.366 Chirality : 0.041 1.969 19499 Planarity : 0.005 0.098 8177 Dihedral : 17.127 179.565 40091 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 30.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.18 % Favored : 91.69 % Rotamer Outliers : 1.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.13), residues: 3742 helix: -0.29 (0.15), residues: 1144 sheet: -0.98 (0.19), residues: 714 loop : -1.80 (0.14), residues: 1884 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 760 time to evaluate : 4.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 39 residues processed: 784 average time/residue: 0.8823 time to fit residues: 1184.5630 Evaluate side-chains 761 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 722 time to evaluate : 4.165 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 39 outliers final: 1 residues processed: 39 average time/residue: 0.6970 time to fit residues: 55.2045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 585 optimal weight: 9.9990 chunk 616 optimal weight: 10.0000 chunk 562 optimal weight: 0.4980 chunk 599 optimal weight: 20.0000 chunk 361 optimal weight: 8.9990 chunk 261 optimal weight: 20.0000 chunk 471 optimal weight: 20.0000 chunk 184 optimal weight: 20.0000 chunk 542 optimal weight: 0.0970 chunk 567 optimal weight: 5.9990 chunk 597 optimal weight: 6.9990 overall best weight: 4.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 14 GLN ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 ASN H 63 GLN ** H 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 HIS ** I 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN ** L 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 HIS ** N 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 35 HIS P 54 GLN R 12 GLN ** T 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 26 ASN ** 1 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.5754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 101964 Z= 0.200 Angle : 0.691 29.738 152487 Z= 0.350 Chirality : 0.040 1.917 19499 Planarity : 0.005 0.073 8177 Dihedral : 16.961 179.000 40091 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 26.14 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.32 % Favored : 92.57 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.13), residues: 3742 helix: -0.34 (0.15), residues: 1144 sheet: -0.88 (0.19), residues: 731 loop : -1.78 (0.14), residues: 1867 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 772 time to evaluate : 4.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 19 residues processed: 788 average time/residue: 0.8778 time to fit residues: 1177.3836 Evaluate side-chains 750 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 731 time to evaluate : 4.270 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 19 outliers final: 1 residues processed: 19 average time/residue: 0.8199 time to fit residues: 31.5332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 393 optimal weight: 0.4980 chunk 634 optimal weight: 4.9990 chunk 387 optimal weight: 7.9990 chunk 300 optimal weight: 0.8980 chunk 441 optimal weight: 40.0000 chunk 665 optimal weight: 50.0000 chunk 612 optimal weight: 20.0000 chunk 529 optimal weight: 9.9990 chunk 55 optimal weight: 30.0000 chunk 409 optimal weight: 6.9990 chunk 324 optimal weight: 7.9990 overall best weight: 4.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 178 GLN ** I 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 GLN ** L 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 35 HIS ** P 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 ASN ** T 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 26 ASN ** 1 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.5846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 101964 Z= 0.195 Angle : 0.694 27.702 152487 Z= 0.352 Chirality : 0.040 2.084 19499 Planarity : 0.005 0.069 8177 Dihedral : 16.875 179.239 40091 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 26.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.16 % Favored : 92.73 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.13), residues: 3742 helix: -0.41 (0.15), residues: 1141 sheet: -0.86 (0.19), residues: 733 loop : -1.72 (0.14), residues: 1868 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 785 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 763 time to evaluate : 5.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 13 residues processed: 774 average time/residue: 0.8786 time to fit residues: 1160.7796 Evaluate side-chains 747 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 734 time to evaluate : 4.196 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 13 outliers final: 1 residues processed: 13 average time/residue: 0.7228 time to fit residues: 21.7973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 420 optimal weight: 6.9990 chunk 564 optimal weight: 8.9990 chunk 162 optimal weight: 30.0000 chunk 488 optimal weight: 5.9990 chunk 78 optimal weight: 20.0000 chunk 147 optimal weight: 20.0000 chunk 530 optimal weight: 20.0000 chunk 222 optimal weight: 30.0000 chunk 545 optimal weight: 7.9990 chunk 67 optimal weight: 20.0000 chunk 97 optimal weight: 20.0000 overall best weight: 9.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 14 GLN ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 ASN ** I 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 35 HIS ** P 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 54 GLN R 12 GLN ** R 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 68 ASN 0 290 GLN ** 0 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.034938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.027573 restraints weight = 710103.838| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 3.68 r_work: 0.2601 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.6140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.085 101964 Z= 0.326 Angle : 0.783 29.585 152487 Z= 0.399 Chirality : 0.044 2.026 19499 Planarity : 0.006 0.091 8177 Dihedral : 17.274 179.586 40091 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 36.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.98 % Favored : 90.91 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.13), residues: 3742 helix: -0.54 (0.15), residues: 1148 sheet: -1.00 (0.19), residues: 722 loop : -1.84 (0.14), residues: 1872 =============================================================================== Job complete usr+sys time: 22532.64 seconds wall clock time: 399 minutes 7.05 seconds (23947.05 seconds total)